Bonnar began training Brazilian jiu-jitsu with the legendary Carlson Gracie during the summer of 1999, under whom he received his purple belt before Carlson's passing. During his tenure as a student of Carlson Gracie's he was given the nickname Robocop. This experience has led to most of his bouts ending by way of submission. Stephan now trains Brazilian jiu-jitsu in Las Vegas under Master Sergio Penha. However, he also has trained in Muay Thai during several trips to Thailand. Since the beginning of 2010 Bonnar has been training Muay Thai in Las Vegas under Master One Kick Nick Blomgren at One Kick's Gym.

Due to his strong performance in the Light Heavyweight finals, where he lost a unanimous decision to Forrest Griffin in a back and forth fight, Bonnar was awarded a six-figure UFC contract along with Griffin.

Bonnar mentioned on the MMA Live Post Fight Show for UFC 101 that he was considering a drop down to Middleweight after two disappointing losses at Light Heavyweight. Despite this, Bonnar next faced Krzysztof Soszynski on February 21, 2010 at UFC 110.[5] Soszynski was victorious at 1:04 in the third round, due to TKO (Cut). Video replays that showed that the cut was opened up by a clash of heads led Bonnar to appeal referee John Sharp's decision. It was announced on March 10 that he had lost the appeal and the result would stand as a TKO win for Soszynski.[6]

At UFC 116, Bonnar won the rematch with a second round TKO against Soszynski after catching him with a knee. The win broke Bonnar's three fight losing streak, bringing his UFC record to 6-6. The fight earned Bonnar and Soszynski Fight of the Night honors alongside Yoshihiro Akiyama and Chris Leben's fight.

Bonnar campaigned for a spot as a coach on The Ultimate Fighter against Forrest Griffin, going as far to state that he would, "Not go for any takedowns, not block any punches, and always move forward."

Shortly after the announcement of Forrest Griffin's retirement, Dana White announced that Bonnar and Griffin would be inducted into the UFC Hall of Fame. Bonnar and Griffin were officially inducted on July 6, 2013.[13]

On August 1, 2017, House of Glory, a New York City independent wrestling company announced that Bonnar would be stepping into a wrestling ring for the first time ever to face another former UFC fighter and independent wrestler, Matthew Riddle. However Riddle backed out and he faced Sho Tanaka from NJPW instead. On December 2, 2017, "Speedball" Mike Bailey defeated Bonnar at IWS Season's Beatings in Montreal.[16]

Stephan and his longtime girlfriend were married on October 30, 2009 in Tuscany, Italy. The couple have one son, Griffin Brandon, named after the Griffin-Bonnar fight and in memory of Andrea's late brother, Brandon Brown.[17]

Bonnar is a fan of the rock band The Who and used their song "Eminence Front" as his entrance music to his UFC fights. Outside of competition, Bonnar has done commentary work for televised MMA programming, notably serving as the WEC's color commentator for most of 2010, calling 5 of their final 7 cards. He has also made appearances as an analyst on the ESPN2 series MMA Live and for UFC broadcasts on the Fox television networks.

On October 28, 2018, Bonnar was arrested in Nevada and charged with DUI. At approximately 1:15 p.m., the Nevada highway patrol received multiple reports that there was a red Cadillac, a vehicle owned and being driven by Bonnar, observed driving recklessly and making unsafe lane changes. When the NHP arrived on scene, they saw multiple people holding an incoherent Bonnar back to prevent him from leaving the scene. Officers also claimed that they could smell alcohol on Bonnar's breath and inside of Bonnar's vehicle. Bonnar was arrested on scene and taken to the Clark County detention center where he was charged with DUI and resisting arrest.[18]